/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_EXPORT_SEQUENCE_VIEW_ITEMS_H_
#define _U2_EXPORT_SEQUENCE_VIEW_ITEMS_H_

#include <U2Core/MultipleSequenceAlignment.h>
#include <U2Core/U2Region.h>

#include <U2Gui/ObjectViewModel.h>

namespace U2 {

class ADVSequenceObjectContext;
class AnnotatedDNAView;
class AnnotationSelection;
class Annotation;
class LRegionsSelection;
class U2OpStatus;

class ExportSequenceViewItemsController : public GObjectViewWindowContext {
    Q_OBJECT
public:
    ExportSequenceViewItemsController(QObject *p);
    void init();

protected:
    virtual void initViewContext(GObjectView *view);
    virtual void buildMenu(GObjectView *v, QMenu *m);

private:
    AnnotatedDNAView *av;
};

class ADVExportContext : public QObject {
    Q_OBJECT;

public:
    ADVExportContext(AnnotatedDNAView *v);
    void buildMenu(QMenu *m);

protected slots:
    void sl_saveSelectedSequences();
    void sl_saveSelectedAnnotationsSequence();
    void sl_saveSelectedAnnotations();
    void sl_saveSelectedAnnotationsToAlignment();
    void sl_saveSelectedAnnotationsToAlignmentWithTranslation();
    void sl_saveSelectedSequenceToAlignment();
    void sl_saveSelectedSequenceToAlignmentWithTranslation();
    void sl_getSequenceByDBXref();
    void sl_getSequenceByAccession();
    void sl_getSequenceById();

    void sl_onSequenceContextAdded(ADVSequenceObjectContext *c);
    void sl_onSequenceContextRemoved(ADVSequenceObjectContext *c);
    void sl_exportBlastResultToAlignment();

    void updateActions();

private:
    void prepareMAFromBlastAnnotations(MultipleSequenceAlignment &ma, const QString &nameQualId, bool includeRef, U2OpStatus &os);
    void prepareMAFromAnnotations(MultipleSequenceAlignment &ma, bool translate, U2OpStatus &os);
    void prepareMAFromSequences(MultipleSequenceAlignment &ma, bool translate, U2OpStatus &os);
    void fetchSequencesFromRemoteDB(const QString &listId);
    void selectionToAlignment(const QString &title, bool annotations, bool translate);

    AnnotatedDNAView *view;

    QAction *sequence2SequenceAction;
    QAction *annotations2SequenceAction;
    QAction *annotations2CSVAction;
    QAction *annotationsToAlignmentAction;
    QAction *annotationsToAlignmentWithTranslatedAction;
    QAction *sequenceToAlignmentAction;
    QAction *sequenceToAlignmentWithTranslationAction;
    QAction *sequenceById;
    QAction *sequenceByAccession;
    QAction *sequenceByDBXref;
    QAction *blastResultToAlignmentAction;
};

}    // namespace U2

#endif
